[gmx-users] How to justify when the trajectory reached equilibrium
lvqingjiejie at 163.com
Fri Jul 10 05:16:11 CEST 2015
> It means to evaluate quantities over successive blocks of time (e.g. using -b and -e that all GROMACS analysis tools support) and check to see whether or not the quantities of interest are varying over time or if they are stable, i.e. converged.
Thank you, Justin.
What size of blocks I need to divide in such an analysis? e.g., for a 100-ns trajectory, is it appropriate to divide it into 5-ns or 10-ns blocks to see if it has converged?
At 2015-07-10 01:39:42, "Justin Lemkul" <jalemkul at vt.edu> wrote:
>On 7/9/15 10:11 AM, Qing Lv wrote:
>> Thank you, Justin.
>> I am trying to simulate a protein-ligand complex to see the conformation transition during the simulation... We propose that the receptor pocket may be subject to a conformational change upon ligand-binding, so I want to verify it by MD...
>> I am really a newbie in molecular simulation and all I did to analysis were time evolution of RMSD, interaction energy, and visualization. I try to do some principal component analysis, but literature said that PCA must be performed after equilibrium...
>If you are hypothesizing a conformational change, then you need a way to
>quantify that change - distances, angles, etc.
>> Could you give me more info on block-averaging, or any other advice that will help?
>It means to evaluate quantities over successive blocks of time (e.g. using -b
>and -e that all GROMACS analysis tools support) and check to see whether or not
>the quantities of interest are varying over time or if they are stable, i.e.
>Justin A. Lemkul, Ph.D.
>Ruth L. Kirschstein NRSA Postdoctoral Fellow
>Department of Pharmaceutical Sciences
>School of Pharmacy
>Health Sciences Facility II, Room 629
>University of Maryland, Baltimore
>20 Penn St.
>Baltimore, MD 21201
>jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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